HsaINT0039607 @ hg19
Intron Retention
Gene
ENSG00000206384 | COL6A6
Description
collagen, type VI, alpha 6 [Source:HGNC Symbol;Acc:27023]
Coordinates
chr3:130363835-130368406:+
Coord C1 exon
chr3:130363835-130363846
Coord A exon
chr3:130363847-130367912
Coord C2 exon
chr3:130367913-130368406
Length
4066 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TAAGGGATATGGTCTTTTAGGAA
3' ss Score
5.53
Exon sequences
Seq C1 exon
CTGGCAGGCATG
Seq A exon
GTGAGTAATCTTTATTTACAGCATGCTTTAATCAAGCTCTAAAATGTCATACATCTGGAAAGATGAGTTAGAGCAATGTATTGGCTTCCAAATGACACAAATTTTATCTGGGCTTTCTTTGCTGCTGCCTCATACTGGTAGCAGAGTCTTGCCTCCAATAAATCACTCAGCTGTAGCTGAGCTTCACAGCTATTTCTCAACCAAGCGATTTGCTTTTTTATTAATAAAAAATCATTAAGATATTAATATCTTAATGACTAACATCACCATTCACCTTGCTTTTAAAGGTTTTAAAAATATGTTGGGGTTTTTTTTAGACATGCTCTGTCACACAGGCTGATCACTGTTCATTGCATTCTTGACCTTCTGGGCTCAAGTGATCCTTCCACTTCAACCTCCGGAGTAGTTGGGACTACAGGCACATGCCATCATGCTTGACTAATTTTTGTATTTTTTGTAGAGGCAGGGTTTTGCCATGTTGCCCAGGCTGGTCCTGAACTCCTGGGCTCAAGTGATCCACCTGCTTTGGCATCTCAAAGTGCTGGGATTACAGGTGTGAGCCACTGTGCCTGGCCAAAAATAGTATTTCTTACTCCCTTCATTTTCTCCCTGTGTCATATCATCTCTGTCATCCAGTGGTTAATTAGGGATTAAGATGCAGAAGGCAGAATAAAAGTGGGGATGATCAGATAGCAAGTAAGTGGAATGTGCAACTCAGATAATGCCAGAATCCATGGAGCTCATGCCTAATGTTAATTATCAAGTTGGCTTCATATTTTTCAGTGCTAGTTTTCAGGTATCTTACAAATGCTTCTTACATGATGTTTTTCTGTAAACTTATCACCCTCTTATACATTTATACACTTTTACCTTTTGTATAAGCCCACAAACCCATGTCCTCTGATTGCTTATCCATGCATTTAAGAATATTTGTTGAAAGCCTAGTAAGTGCCAGTATGTGTAGTAGGCATTAGGGATACAGAGTTGAATAATGAATCTGCTTCCTGTGCTCAGAAACTTCCATTCTTATGGAGGATCCAGATCACAAACAAATAAACAAAGGGAAGCCCAGCACATTAGGTGCTATTTGAAAGAGATAACCTGCACATTGTGCACATGTGCCCTAAAACTTAAAGTATAATAATAATAAAATAAAAAATAGAAAGAGATAAAGCATAGGATGCTGTGTCCTGGGATAATGTAAGGGGGGGAGATGTTTTTGGACAGAGGGCTCTTTTTGGGGGCAGTGAAATTAAAGTTTAGACTGAAGAACACAAAGGAGCTGTCTTTTGGCTGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTGGGAGCCCGAGGCAGGCAGATCACGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATAGTGAAACCCCATCTCTACTAAAAATACAAAAAATTAGCTGGGCGTGGTGGCACATGCCTGTAATCCCAGCTGCTTGGGAGGCTGAGGCAGGAGAATCACCTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATCACACCACTGCATTCCAGCCCGGGTGATAGTGTGAGACTCCGTCTCAAACAAAAAAAACCAAAGGAGCCATCTTTCAAGAGCTGGGCATAGGGAACTTTAAGTGCAAAGGCCATGAAACAGAACAGACCTGGGTATTTCCTAGGAACTGATGGAGCCCAACAAGGTTGAGACATAGGGAGGGGGAGAGTAGTGCATAAAAACATGGGGAATAGGCAAAGGCCAGAGCAAGCTGAGCTTTGCACATTATAAGGAGGCTGGATTTTATTTGAGTTGTGATGGGGTGGGTATTAAAGAGTATGTTGAAAGTATGTAGGGGAGGAGCATGATCTGATTTTAAAATATTACTTGGGCTGCTATGGGGAGAGTGGATTGTGGCAAGGGTGAAGGGTAGGAAATGTCAAAGCCAAAGGCCTAGTTTAGAGAGGACTGTAGTATTCAGGCAAATATGGTGGCGACCTGGATAAGGACCATCAGTGTTGTGTTTAGGTTACATGGCAGTGGTTTGGGCTGATCCTTGCCTCCCTGTTCTTTTTTTCACCTCCTCTGTGGCAAGTAGCAGTCCTCAGTACATAGTGTGAGGTCACAGAGCCATGTTAGTTGGGGAACCGCACATGGCAATCCTTCCCTTTTTGAGGAGGGCCTCCTAGGTACCACTGCCATCCAGCCTAGGCTTCTTCAGAATCCTTGGGATTCCTGGCAGCTTGCTTGGTTTTTAGGGCTTGTGTTTTGGAAGCTGAATTAGTCCTTAGGTTTTTCCCCTAAAAAAACTTGAATTTTTTTTTCATATCTTCAGCCAGTGCTGTGAACCTTCACCCACCCTTCTCTCTAAATTGTATCTGAAGCATTTTTGTTGTTGTTTCCATGTGCAAATAACCACCCCCCAAAAAATCAGAAGAATCACTTTCATGTTTAGTTCTACTGACTTTTTTAAACGATAAAAGTGACACGTCCATTTATAAAAATCTGTTCAGCCCAGTAATTTAGACTTAGAGACTAATACATGATTTCCTGTCTCCATCGAGATGAACAGTTTGATTTGGGTTTGAACATTTATTCTCACTGGTACTTCTTTTGCCTTTGAAGGACATGGAGTCAAGGACGGGAGGAGGTCATAGTTTAGCACTAAGGTGGGCAAGGCCCAGTTGGCCCATGGCAGAGGGATGTCTCCTTGCCAGCCTACGTGAGCCCCAGCAAGTCTGAGTTCCTGAGCTTGTTGTAAAGCAAGATGGTCTTTGCTGTGTTTATTATCTCTGAATCTGACTTGCTGATATCTGAATGAGAGGAGGCACCTCTCCAAGAGAAACACATCACTGGGGTGTCCTTTTACCAACCAAATCCCAGCACTAGGCATCTCACGTATTATTAAACTTTTGTTATTTCTATACCTGTTGCAAAGAACTGCTCTTTGTTGAGCTCTTTTTCATTCATTCAGCATTTGTTAGATATCTGATATATGGCAGGGACTAATAACTTAGAAGGTCAGCAGATCCTCTTCCTATCCATGCATCATAAACTAGGATAAATGAACATTAATCAGATAATCAAAAATAAGTTATCAACTGTGACAAGTGCAAAGTACCGAAATTAGAATGATTTGGAACCAATGAGTATGGATGCATAAATATGCAATTAACACTTACAGTAGAGTTTACCAACCATAATCAGTTTCTCTAAGTAATAAGGCATATTTATTGAGTAAACTTGCATTTGTAACTGTTAAACAAAAATGTATCTGTTAAAGCTTTCCTCAGTCTCCTTTTAGTGATGTATTTCTCACAATGAAAAAGTCTGGAATGATAATTATAACAGCAATGGTTGACATTTATTGAGCACCTACTATGTGCCAGGTTCTGTTATTCTAAGTACTTTACCTGTGCTGATTCATTTAATGCTCACCTCAGGCCTATGTAGCAGGTGATGTTATGACTCACATTTTACAGATGAAGAAACTGAGGCACAGACAGGATGAGTAATTCAGACAGGGTCACATGGCTGGTTAGTGATTGGGCCAGGGCGCTAAACTCTACCCTGTATTGCCTACTCTCTTTGCGTCTCATTCTTTGCTCTGTAAATTATGTCAGTTTTCTTCCAATTTTTCTAAAATTATCAGAGCTTTCACAGCCTTTCCTTTTTAACTCTTATTACATTTCCTTATTAAGTAAAAAAAGAAATGTGTTTAACTGAGTGAAGTTCCAGCAACAAAACTTGATACTTTTGATCGAGTCTCTGCAGGTGAAGGGTATTTCCAGGAGCTCTCTATTGTTTAGAAGGAATTTGATAATGAACTTTAACATTTCATATAAAATAAAACTGAATTCCAGATGTTTTCCTTTTGTGCTTGATTCAAAAGAGCAGACTCAGCTTTTGGAATAACATCTATAATTATTCAAGATTTAAATATATTTTACATGTTTGTTTTAATACTTAAATTATTCTCTTTAAGTATTTGAATGCTTAACATTTAAAATTACTTTGCCTTCTATGTATCTTTTTTTTTTTTTAAATAAGGATGCTATGTGTTAAGGGATATGGTCTTTTAG
Seq C2 exon
GAAAACCGGAATGCCCAGTGCACCCAACCGAGTTGGTGTTTGCCCTGGACCACTCCCGGGATGTCACTGAGCAGGAATTTGAGCGGATGAAGGAGATGATGGCTTTCCTGGTGAGAGACATTAAGGTCCGGGAGAACAGCTGCCCCGTGGGAGCGCACATCGCCATCCTCTCCTATAACTCCCACGCCAGGCACCTTGTGCGCTTCTCAGACGCCTACAAGAAGAGTCAACTTCTCAGAGAAATTGAAACTATTCCTTATGAGAGATCCTCTGCCAGCAGGGAGATTGGCAGAGCAATGCGGTTTATTTCCAGGAATGTCTTCAAGCGGACGCTTCCGGGGGCACACACGAGAAAAATCGCCACATTTTTCAGCAGCGGTCAGTCCGCGGATGCCCACTCCATCACCACGGCTGCCATGGAGTTCGGCGCGCTTGAAATCATTCCCGTGGTGATCACTTTCAGCAACGTGCCCTCGGTCAGGCGCGCATTTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206384-COL6A6:NM_001102608:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.079
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(94.5=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)